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Jvarkit : Java utilities for Bioinformatics
By Jit 3040 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics
Tools to access the quality of your assembled genome !
Last updated 786 days ago by LEGEFASTA VALIDATOR + SEQKIT RMDUP: FASTA validation GENOMETOOLS GT GFF3VALIDATOR: GFF3 validation ASSEMBLATHON STATS: Assembly statistics GENOMETOOLS GT STAT: Annotation statistics NCBI FCS ADAPTOR: Adaptor contamination pass/fail NCBI...LSC :a long read error correction tool
By Jit 2985 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2938 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 3056 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads
By Jit 2441 days agobioinfo.ut.ee - FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 2108 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 3090 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...-
SPAdes hybrid genome assembly
Last updated 3233 days ago by Jit Comments (1)When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the... String graph based genome assembly software and tools !
By Rahul Nayak 3210 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.
